July 13, 2005

Jonathan Witt Should Read Before He Writes

Responding to George Will's excellent column on "A debate that will does not end," Discovery Institute Senor Fellow Jonathan Witt, Ph.D. in English, writes to Newsweek,

George Will says the theory of intelligent design isn't falsifiable - isn't a "testable hypothesis." Actually, particular design arguments are falsifiable. Design theorist Michael Behe, for instance, argues that we can detect design in the bacterial flagellum because the tiny motor needs all its parts to function at all. That's a problem for Darwinian evolution, which builds novel form one tiny functional mutation at a time. How to falsify Behe's argument? Provide a detailed evolutionary pathway from simple ancestor to present motor. The flagellum might still be designed, but Behe's argument that such design is detectable would have been falsified. [Newsweek July 7, 2005, 19-20]

Anyone reading this letter and not knowing much biology, and that is most readers, would think that there has been no attempt to falsify Behe's flagellum argument. Of course, they would be wrong. And a major part of the falsifying evidence and argument is exactly what Witt asks for. All he'd had to do is go to TalkOrigins and search for flagellum. The very first hit debunks Behe's argument from three different directions. The first one is exactly what Witt demands.

One plausible path for the evolution of flagella goes through the following basic stages (keep in mind that this is a summary, and that each major co-option event would be followed by long periods of gradual optimization of function):

a) A passive, nonspecific pore evolves into a more specific passive pore by addition of gating protein(s). Passive transport converts to active transport by addition of an ATPase that couples ATP hydrolysis to improved export capability. This complex forms a primitive type-III export system.

b) The type-III export system is converted to a type-III secretion system (T3SS) by addition of outer membrane pore proteins (secretin and secretin chaperone) from the type-II secretion system. These eventually form the P- and L-rings, respectively, of modern flagella. The modern type-III secretory system forms a structure strikingly similar to the rod and ring structure of the flagellum (Hueck 1998; Blocker et al. 2003).

c) The T3SS secretes several proteins, one of which is an adhesin (a protein that sticks the cell to other cells or to a substrate). Polymerization of this adhesin forms a primitive pilus, an extension that gives the cell improved adhesive capability. After the evolution of the T3SS pilus, the pilus diversifies for various more specialized tasks by duplication and subfunctionalization of the pilus proteins (pilins).

d) An ion pump complex with another function in the cell fortuitously becomes associated with the base of the secretion system structure, converting the pilus into a primitive protoflagellum. The initial function of the protoflagellum is improved dispersal. Homologs of the motor proteins MotA and MotB are known to function in diverse prokaryotes independent of the flagellum.

e) The binding of a signal transduction protein to the base of the secretion system regulates the speed of rotation depending on the metabolic health of the cell. This imposes a drift toward favorable regions and away from nutrient-poor regions, such as those found in overcrowded habitats. This is the beginning of chemotactic motility.

f) Numerous improvements follow the origin of the crudely functioning flagellum. Notably, many of the different axial proteins (rod, hook, linkers, filament, caps) originate by duplication and subfunctionalization of pilins or the primitive flagellar axial structure. These proteins end up forming the axial protein family.

How much more detail does Witt want?

And then TalkOrigins gives very specific evidence,

The bacterial flagellum is not even irreducible. Some bacterial flagella function without the L- and P-rings. In experiments with various bacteria, some components (e.g. FliH, FliD (cap), and the muramidase domain of FlgJ) have been found helpful but not absolutely essential (Matzke 2003). One third of the 497 amino acids of flagellin have been cut out without harming its function (Kuwajima 1988). Furthermore, many bacteria have additional proteins that are required for their own flagella but that are not required in the "standard" well-studied flagellum found in E. coli. Different bacteria have different numbers of flagellar proteins (in Helicobacter pylori, for example, only thirty-three proteins are necessary to produce a working flagellum), so Behe's favorite example of irreducibility seems actually to exhibit quite a bit of variability in terms of numbers of required parts (Ussery 1999).

Eukaryotic cilia are made by more than 200 distinct proteins, but even here irreducibility is illusive. Behe (1996) implied and Denton (1986, 108) claimed explicitly that the common 9+2 tubulin structure of cilia could not be substantially simplified. Yet functional 3+0 cilia, lacking many microtubules as well as some of the dynein linkers, are known to exist (Miller 2003, 2004).

TalkOrigins has even more.

It is simply irresponsible for Witt to write such a letter using as his only example a completely discredited idea.

While Witt has packed a lot of nonsense into a single short paragraph, there are just a couple of other points I would like to address. Contrary to what one might think from Witt's letter, intelligent design creationism is not based on things like Behe's claim; it is based on a series of naive intuitions that are looking for something that has the appearance of support to the holder of such naive intuitions. If you don't believe me look at the "escape clause" with which Witt ends the letter,

The flagellum might still be designed, but Behe's argument that such design is detectable would have been falsified.

In fact, there are no falsifiable claims made by intelligent design creationists that would falsify intelligent design creationism for them. The few such claims they have made have all been shown to be false or based on faulty logic or both. But there are thousands of such claims that biologists make on a regular basis that, if falsified, would bring down the current synthesis.

Finally, George Will does say, "The problem with intelligent-design theory is not that it is false but that it is not falsifiable. . ." And despite Witt's letter, Will is correct. The often-repeated set of claims of Behe's idea is one, do not make a scientific theory; they are just a set of incorrect surmises. No number of incorrect surmises adds up to a scientific theory. The "theory", if you want to call it that, is that some designer created all or major parts of the biological diversity we see around us. And that "theory," based as it is on faith, is not falsifiable. Witt's escape clause is strong evidence that I am correct on this point.

It would be helpful if the folks at the Discovery Institute, would stop bringing up the same discredited arguments and instead read, and react to the real evidence. They might just discover something.

Posted by DuaneSmith at July 13, 2005 09:44 PM | Read more on Evolution |

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Intelligent Design should never have been introduced as a subject for debate by the IDists. ID is a given without which nothing in evolution will ever make any sense. Living things are machines and WERE designed. Just as machines are specified with blueprints, so both ontogeny and phylogeny have had their blueprints as as well. For evolution those blueprints have apparently all been read and implemented with evolution now limited to the production of varieties and subspecies. These phenomena are indeed the result of selection, natural or artificial, but macroevolution, no longer in progress, resulted largely if not entirely from endogenous forces the nature of which remain unknown but in my opinion, and that of Pierre Grasse and Leo Berg, undeniable.

These considerations, about which I remain convinced, provide the basis for the "Prescribed Evolutionary Hypothesis," Rivista di Biologia 98(1): 155-167, 2005.

Posted by: John A. Davison at July 14, 2005 07:52 AM

I am surprised that my post has not created some reaction. We critics of Darwinism have always been ignored. Perhaps this is just one more example.

Posted by: John A. Davison at July 18, 2005 03:49 AM

Here are my comments from PandasThumb:

Jonathan Witt has a Ph.D. In English. But he’s not very good with it, as he demonstrates when he refers to specific instances of things claimed to be designed as “particular design arguments”. Nor does he do well with theory of science or with logic. It is empirical claims, or theories with empirical implications, not “arguments”, that are falsifiable. Behe’s claim is that recognition that the flagellum could not have evolved constitutes detection of design. Aside from the fact that this is blatant argumentum ad ignorantiam and sticks human psychology in the middle of biological theory, showing that the flagellum might have evolved would only show that design was not detected in this case, so it doesn’t “falsify” any theory. But it would refute Behe’s claim that the flagellum is IC, or that IC isn’t achievable by evolution. Except that this claim has been refuted numerous times, above and beyond the fact that Behe has never shown the good faith of accepting the burden of proof that attaches to those who make claims. Jonathan Witt also doesn’t do well with the theory of evolution; he knows, or should know, because it’s been explained numerous times already, that “needs all of its parts to function at all” is not “a problem for Darwinian evolution”, and that the claim that “Darwinian evolution … builds novel form one tiny functional mutation at a time” is nonsense; mutations are at least as likely to alter or destroy existing form as they are to create novel form. Behe and Witt construct absurdly constricted rules as to the effects of mutations, label this silly strawman “Darwinian evolution”, and then complain that it can’t do the job. This has nothing to do with science, which builds theories as it goes that describe how things actually are, according to the evidence, rather than setting up some a priori “theory” as a fixed set of rules and then tossing it out when it doesn’t fit the facts. That’s why the theory of evolution itself has “evolved”.

So, given that he lacks relevant qualifications, competence, knowledge, and ethics, why is Jonathan Witt given any credence at all?

Posted by: ts at July 21, 2005 02:05 AM

in my opinion

Hi Professor,

May I suggest that lack of a reaction may be due to the lack of content in your post. Where do you see the evidence for the various assertions that you have made over the years?

Posted by: Alan Fox at July 21, 2005 04:28 AM

There is as yet no evoltionay theory, only failed and untested hypotheses. Darwinism and Lamarckism are examples of the former and the Prescribed Evolutionary Hypothesis is an example of the latter. Darwinism in all its trappings remains the most thoroughly tested and failed hypothesis in all of biological science. It had absolutely nothing to do with creative evolution beyond the production of varieties and subspecies. To continue to claim that it did is scandalous.

Posted by: John A. Davison at July 21, 2005 04:32 AM

More assertions. Evidence?

Posted by: Alan Fox at July 21, 2005 04:35 AM

Mendel's experiments, truly unique contributions to biological science, were ignored for 32 years until, long after his death, they were finally accepted when something was finally recognized that occurred as pairs, namely the chromosomes. Some of us now realize that the chromosomes, not the genes, are the real instruments of evolutionary progress as it is becoming increasingly more evident that evolution has involved the release from latency of preformed, front-loaded information which was there from very early on in the evolutionary sequence or more likely sequences. That is exactly how ontogeny functions today by the controlled release from latency of information that must have been present in the fertilized egg. Ontogeny remains a powerful model for phylogeny. Both have have involved the derepression of preformed information, a process which has in no way involved the environment beyond its possible role as a releaser. In short, both processes proceeded driven by internal forces which as yet have not been identified but whose existence can no longer be questioned except by ideologues who are congenitally incapable of recognizing reality.

As for my own contribution to the great mystery of evolution, it is little more than the natural extension of the independent insights of several of the most penetrating minds of two centuries, every one of whom saw through the Darwinian hypothesis and identified it as a total failure.

Darwinism in all its many guises remains the most failed hypothesis in the history of science. Soren Lovtrup called it a deceit. I call it a hoax.

As for evidence, it is the lack of it that has doomed Darwinism. The time honored method of the elimination of all alternatives has driven me to the only reasonable remaining explanation, an explanation that remains in complete accord with everything we really know about the greatest mystery in all of biological science, the origin, or more likely origins, and the subsequent history of those origins, a history which seems to have run its course.

I don't expect anyone to take my word for it so I offer the independent appraisals of some of my distinguished sources, not a Darwinian in the lot.

"Evolution is in a great measure measure an unfolding of pre-existing rudiments."
Leo Berg, Nomogenesis, page 406

"Finally, Bateson likewise (1914, p. 640) inclines to the view that the entire process of evolution may be regarded as 'an unpacking of an original complex which contained within itself the whole range of diversity which living things present'."
ibid, page 359

"However that may be, the existence of internal factors affecting evolution has to be accepted by any objective mind..."
Pierre Grasse, The Evolution of Living Organisms, page 209

"At most, the environment plays only a similar role with regard to organisms; IT CAN ONLY PROVOKE AND SET IN MOTION SOME POTENTIAl THAT IS ALREADY PRESENT."
Otto Schindewolf, Basic Questions in Paleontology, page 312 (his emphasis)

To continue to deliberately and cynically ignore these scientists constitutes nothing less than a scandal, one unprecedented in the history of science.

Ask not for whom the bell tolls. It tolls for neoDarwinism.

"Meine Zeit wird schon kommen!"
Gregor Mendel

Posted by: John A. Davison at July 21, 2005 07:55 AM

No-one questions the contribution of Gregor Mendel to Science (except for whispers that some of his later results were "too good to be true"). Are you comparing yourself with Gregor Mendel?

Chromosomes are real structures that contain DNA which in turn carries reproducible information sequentially in the triplet base code. A gene is a length of that sequence. How can one say the chromosomes, not the genes, are the real instruments of evolutionary progress?

Darwin made an enormous contribution to evolutionary biology that has created a framework for subsequent interlinking discoveries and theories. There is a huge body of evidence and for you to claim otherwise as a former professor of biology is, frankly, amazing.

Your front loading theory (hypothesis, or perhaps untested hypothesis might be more accurate) seems prone to the same "reductio ad absurdum" argument as the older idea of the Homunculus.

Posted by: Alan Fox at July 21, 2005 09:27 AM

Alan Fox

First of all I have no theory. There is at present no theory of evolution, only failed and untested hypotheses. I have offered one of the latter and it isn't even entirely mine. As I have published, the idea of a prescribed evoluion can be traced back first to William Bateson, then to Reginald C. Punnett, then to Leo Berg, next to Otto Schindewolf, next to Pierre Grasse and finally to myself. Furthermore, such an hypothesis may not even be testable directly just as Schindewolf suggested. Nevertheless, the great antiquity of many gene families which until recently were thought to be of mammalian origin clearly favors this hypothesis. So does everything we know from chromosome structure and physiology. There is not a shred of evidence that allelic mutation has ever played a role in creative evolution. The entire mutation/selection scheme of neoDarwinism is a myth without foundation.

The simple undeniable truth is that there is not a single tangible piece of evidence implicating the environment in producing any progressive evolutionary change beyond the variety or subspecies. The only thing that seems undeniably certain is that evolution proceeded independent of the environment just as ontogeny does today. The fundamental error that the Darwinians still continue to make is that evolution has or had an exogenous cause. Such a cause has yet to be identified and, until it has been, I maintain that such a cause never existed beyond acting as a trigger for an innate latent potential. If you or others are willing to continue ignoring the independent conclusions of scientists of the caliber of Pierre Grasse, William Bateson, Leo Berg, Otto Schindewolf and Reginald C. Punnett, in favor of the empty speculations of such self-proclaimed armchair experts as Ernst Mayr, Stephen Jay Gould, William Provine, Francisco Ayala and Richard Dawkins, there is nothing that I can or further choose to do for you. I come to forums in the same spirit that I publish my papers. It is to enlighten. I get only negative responses from amateurs most of whom insist on anonymity. I am still waiting for the professionals to respond in hard copy to the challenges presented by myself and my many distinguished predecessors all of whom have identified neoDarwinism as an intellectual and scientific disaster. Darwinism, without question, is the most thoroughly discredited hypothesis in the history of science. It persists only for ideological reasons which, in all probablility, as has already been demonstrated for our political views, has a genetic basis. The way we look at the world is just one more manifestation of a prescribed and predestined evolution.

"Everything is determined... by forces over which we have no control."
Albert Einstein

You have your intellectual sources and I have mine. I regard mine with the highest respect and have no intention of abandoning them. It is as simple as that.

Posted by: John A. Davison at July 21, 2005 12:45 PM

Professor Davison

Are you using some sort of automated respose syatem?

Posted by: Alan Fox at July 21, 2005 03:17 PM

Actually, John, you old fart, don't you miss the sparkling repartee of Pandas thumb?

Posted by: Alan Fox at July 21, 2005 03:34 PM

Alan Fox
The cowards at Panda's Pathetic Pollex, led by Esley Welsberry, banned me, hopefully for life from any further participation in that snake pit.

I cherish that award right along with similar honorifics from ARN, EvC, The Austringer, Uncommon Descent, ISCID's "brainstorms" (what a misnomer), A Physicists Perspective, Pharyngula and FringeSciences. I am sure I have overlooked a few. I also understand I have been granted the "Crankiest" prize for which I am not only pleased but delighted.

For some reason John Rennie still allows me to post at SciAm Perspectives where I have unanswered posts at several threads. He is practicing the time honored method adopted by Darwinians for decades. They just pretend their critics do not exist. It is easier for them that way don't you know.

When I am ignored and worse, denigrated and ridiculed, it is for exactly the same reason that Pierre Grasse, William Bateson, Richard B. Goldschmidt, Leo Berg, Reginald C. Punnett, Robert Broom and Otto Schindewolf also continue to be ignored. Both collectively and individually we have destroyed Darwinism many times over. The Darwinians are congenitally incapable of recognizing that they are chasing a phantom and always have been. The only remaining alternative, that evolution was a planned and predetermined sequence, simply cannot penetrate their ideologically and genetically barricaded brains. It is really not their fault as it is just another manifestation of a prescribed evolution. Don't take my word for it. Just consider the opinion of another, like myself, a convinced determinist. I can only hope that you have more respect for him than you have for me and the many distinguished sources on whom my contributions so heavily depend.

"Our actions should be based on the ever-present awareness that human beings in their thinking, feeling, and acting are not free but are just as causally bound as the stars in their motion."
Albert Einstein

It is hard to believe isn't it?

As I used to say over at EvC before Percy couldn't stand it any more - Who is next?

Posted by: John A. Davison at July 22, 2005 04:43 AM

Sorry, comments are closed for this post.
Send me an email if it is important.